Coastlooc data paper

Data cleaning and pre-processing

This section shows the main steps that have been applied to pre-process the raw data.

aCDOM spectra

  • The CDOM spectra were modelled according to the information in @.

    • acdom spectra were re-fitted using the complete data (i.e. between 350-500 nm) because the data in all_abs_transpose.txt started at 380 nm.

  • Average background values calculated between 683-687 nm and subtracted from each spectrum.

  • Some files were in binary format, so I could not open them (ex.: C2001000.YSA).

  • Some spectra start at 300 nm while others at 350 nm.

  • Calculated the correlation between the measured and the fitted values.

    • Fits with R2 lower than 0.95 were removed from the data.

  • Absorption spectra with any negative values below 500 nm were removed.

  • Exported the complete spectra (350-700 nm): both the raw and the modelled data.

Phytoplankton and non-algal absorption

  • Absorption spectra with any negative values below 500 nm were removed.

Irradiance

  • There were negative values in the irradiance data (Ed, Eu, Kd, Ku). I have cleaned the data by setting these negative values to NA.

  • Eu is in fact Eu0- that was estimated using a two-exponential function model.

  • Ed is in fact Ed0- calculated from 0.94 x ed0+.

  • There are differences in wavelengths among cruises. I have not found any information in the report concerning channel change across the missions.

A2 C1 C3 C4 C5 C6
411 411 411 411 411 411
443 443 443 443 443 443
456 456 456 456 456 456
490 490 490 490 490 490
509 509 509 509 509 509
532 532 532 532 532 532
559 556 559 559 559 559
619 590 619 619 619 619
665 665 665 665 665 665
683 683 683 683 683 683
705 705 705 705 705 705
779 779 779 779 779 779
866 866 866 866 866 866
A2 C1 C3 C4 C5 C6
559 556 559 559 559 559
619 590 619 619 619 619

Reflectance

  • Reflectance values outside the 0-1 range were set to NA.

Other stuff

  • Extracted extra variables (DOC, AQY) from Massimo 2000.

Bathymetry

  • I have extracted the bathymetry at each sampling locations.

Journal candidates

Figures for the paper

This section shows the figures that I think should be included in the data paper.

Figure 1

Figure 1: Map of the sampling stations.

Figure 2

Figure 2: (A) Overview of the temporal sampling for the seven areas. The numbers in the circles indicate the number of visited stations each month. (B) Boxplot showing the bathymetry at the sampling locations by area.

Figure 3

Figure 3: (A) Total chlorophyll-a and (B) particulate organic carbon across the sampled areas.

Figure 4

Figure 4: (A) Average total particulate (\(a_\text{p}\)), (B) non-algal (\(a_\text{NAP}\)), (C) phytoplankton (\(a_{\phi}\)) and (D) chromophoric dissolved organic matter (\(a_\text{CDOM}\)) absorption spectra in each area. (E) \(a_\text{CDOM}(350)\) along the westernmost transect in the North Sea (see Fig. 1B).

Figure 5

Figure 5: (A) Particulate scattering coefficient at 440 nm (\(b_{b}(440)\)) and (B) attenuation coefficient for downward irradiance at 443 nm (\(K_{d}(443)\)) across the sampled areas.

Figure 6

Figure 6: Spectra of downward irradiance measured at the surface across the sampled areas. The tick lines represent the average spectra.

Figure 7

Scatterplots showing relationships among different selected variables. (A) Particulate organic carbon (POC) and (B) phytoplankton absorption at 443 nm (\(a_{\phi}(443)\)) against total chlorophyll-a. (C) Downward irradiance at 443 nm (\(E_{d}(443)\)) and (D) particulate scattering at 440 nm (\(b_{b}(440)\) against particulate organic carbon. The red lines show the linear relationships between the variables. The shaded gray areas represent the 95% confidence intervals around the fitted models.

Appendix 1

Example of extrapolation of the upward irradiance towards the sea surface. The irradiance values just below the sea surface and the corresponding diffuse attenuation coefficient for the topmost water layer are specified in the figures.

Done

  • Validated that there are no absorption for Med. Sea Case 1 cruise.

  • A few stations were located on the land (bad geographical coordinates). They have been removed.

  • Calculate s_nap and s_cdom. See the method in Babin (2003) where he removes some wavelengths to calculate s_nap.

  • Removed dissolved a and c from the AC9 data because there were problems with the filtering procedure during the sampling. These correspond to the ad and cd variables in SurfaceData5(C4corr).txt.

  • Extract bathymetry at each station.

  • Zoom on geographic areas in Fig. 1 such as figure 13 in the final report.

  • Recode Ed wavelengths from the SPMR vertical profiles as:

    • 412 -> 411
    • 510 -> 509
    • 589 -> 590
    • 666 -> 665
    • 780 -> 779

  • Validated that are only two AC9 measurements in the Adriatic Sea.

  • Removed duplicated radiometric surface spectral profiles (duplicated Ed/Eu/Kd/Ku).

TODO

  • Use piggyback https://docs.ropensci.org/piggyback/

  • Release the final report PDF with a DOI and cite it in the main text.

    • Who should be included in the release of this document?

  • Make sure that SPMR units are OK. um vs nm. Change accordingly in the SPMR code file (zzz_radiometer.R).

  • SPMR vertical profiles have been reprocessed. This means that the original surface data is not the same as the newly processed vertical profiles (i.e. extrapolation to the surface). How to deal with that?

References

Babin, Marcel. 2003. “Variations in the Light Absorption Coefficients of Phytoplankton, Nonalgal Particles, and Dissolved Organic Matter in Coastal Waters Around Europe.” Journal of Geophysical Research 108 (C7): 3211. https://doi.org/10.1029/2001JC000882.